Variant report

Variant	rs62344543
Chromosome Location	chr4:151229881-151229882
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:151229188..151230723-chr4:151231370..151233714,2	K562	blood:

Variant related genes	Relation type
ENSG00000198589	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11722135	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723398	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728745	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734641	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734677	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734774	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11737203	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11737450	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1507190	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1507191	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17503964	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17504117	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17588629	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2056457	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35750119	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4696083	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696084	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696087	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696299	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs55889963	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56004102	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56198556	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56374126	0.98[ASN][1000 genomes]
rs56398631	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58138000	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59713336	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60105956	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60459852	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61269060	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62344542	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62344544	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62346984	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62346985	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62346990	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67227188	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834124	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72734403	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv880257	chr4:151170387-151231371	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv880259	chr4:151210761-151367745	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv880260	chr4:151214038-151331191	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv817540	chr4:151228965-151858609	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62344543	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151191400-151245200	Weak transcription	Small Intestine	intestine
2	chr4:151192400-151232800	Weak transcription	Brain Substantia Nigra	brain
3	chr4:151203800-151244400	Weak transcription	Fetal Thymus	thymus
4	chr4:151204000-151244600	Weak transcription	Lung	lung
5	chr4:151204600-151236000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:151204600-151242200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:151205000-151236400	Weak transcription	Primary B cells from cord blood	blood
8	chr4:151205000-151272200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:151207600-151241600	Weak transcription	Fetal Intestine Large	intestine
10	chr4:151208000-151230400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr4:151208600-151230400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr4:151210800-151231400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:151211200-151236200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:151213400-151242200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:151213600-151231000	Weak transcription	Primary T cells from cord blood	blood
16	chr4:151213800-151236200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:151221800-151231200	Weak transcription	Fetal Heart	heart
18	chr4:151221800-151236200	Weak transcription	Left Ventricle	heart
19	chr4:151221800-151259600	Weak transcription	Fetal Intestine Small	intestine
20	chr4:151223200-151237600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:151223800-151237800	Weak transcription	Pancreas	Pancrea
22	chr4:151224000-151259000	Weak transcription	Ovary	ovary
23	chr4:151224200-151230800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:151224200-151237600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr4:151224200-151244800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:151224200-151274800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:151224400-151232000	Weak transcription	K562	blood
28	chr4:151224400-151236000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:151224400-151236000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:151224400-151244600	Weak transcription	NHLF	lung
31	chr4:151225000-151241400	Weak transcription	GM12878-XiMat	blood
32	chr4:151226000-151249000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr4:151226200-151230600	Enhancers	HMEC	breast
34	chr4:151226200-151240600	Weak transcription	Fetal Kidney	kidney
35	chr4:151226400-151236000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:151226600-151231000	Strong transcription	Primary hematopoietic stem cells	blood
37	chr4:151226600-151231600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:151226600-151236200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:151226600-151242400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:151226800-151272400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:151227200-151230800	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:151227200-151232400	Enhancers	HUVEC	blood vessel
43	chr4:151227400-151230800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr4:151227400-151231400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:151227400-151231600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:151227400-151269400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr4:151227800-151231000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:151227800-151248400	Weak transcription	Adipose Nuclei	Adipose
49	chr4:151228000-151230800	Weak transcription	Liver	Liver
50	chr4:151228000-151237600	Weak transcription	Brain Anterior Caudate	brain

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